Release Notes

TASQ 2.2

1870444

Release Notes
for

TASQ 2.2

Language: en

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Release Notes
TASQ 2.2

Contents
1 Overview ................................................................................................................................ 4
2 TASQ 2.2 features ................................................................................................................. 4
3 Installation procedure ............................................................................................................ 5
3.1 Initial installation of TASQ ................................................................................................ 5
3.2 TASQ server / workstation requirements ......................................................................... 5
3.3 TASQ server / workstation installation ............................................................................. 6
3.4 TASQ client installation .................................................................................................... 7
3.5 Licensing TASQ .............................................................................................................. 10
4 Site specifications and data security ................................................................................... 11
4.1 Compatibility issues ........................................................................................................ 11
4.2 Data format issues .......................................................................................................... 11
4.3 Security issues................................................................................................................ 11
4.3.1 Network connection ................................................................................................ 11
4.3.2 Antivirus software.................................................................................................... 12
4.3.3 Firewall issues ........................................................................................................ 12
5 Manuals ............................................................................................................................... 12
6 Known problems / bugs ....................................................................................................... 13
6.1 Database systems have been updated — incompatibilities ........................................... 13
6.2 Batch processing fails ..................................................................................................... 13
6.3 No more licenses left ...................................................................................................... 15
6.4 Update problems in Chromatograms view ..................................................................... 15
6.5 Working with different methods ...................................................................................... 15
6.6 No results although processing was successful ............................................................. 16
6.7 Import of tasqMethod fails .............................................................................................. 18
6.8 TASQ client crashes when a report is generated ........................................................... 20
6.9 Quantitation view does not show a calibration function and calibration table is empty.. 20
6.10 If no concentration for an internal standard is specified, the data point will not be
taken into account for regression calculation or no quantities can be calculated for
this determination ........................................................................................................... 20
6.11 HyStar cannot start sequence of TASQ batch if tasq processing service is not
started ............................................................................................................................. 20
6.12 Chromatographic peaks are not centered in reports ...................................................... 21

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6.13 Exporting of large tables containing icons to Excel file format is time consuming ......... 22
6.14 Processing data on a network drive ............................................................................... 22
6.15 Running TASQ TQ-Batch Processor on a remote computer ......................................... 22
6.16 Running automatic reporting feature does not work for TOF workflow .......................... 22
6.17 Exporting result data to LIMS in automation .................................................................. 22
6.18 Analytes with expected retention time = 0 are scored with failed for RT Score
instead of RT Score not available (grey) ........................................................................ 23
6.19 If Ion Ratio deviates too much from expected Ion Ratio the Ion Score renders red
also for TOF data sets .................................................................................................... 23
6.20 Sometimes the GUI got scrambled................................................................................. 24
6.21 Installation of TASQ and/or MCube server setup seems to be frozen ........................... 24
6.22 After upgrading TASQ server the Bruker Compass Server does not start timely .......... 25
6.23 Upgrade to TASQ method version 2.2 alters smoothing width ...................................... 25
7 Reporting bugs to Bruker ..................................................................................................... 26

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TASQ 2.2

1 Overview
This document provides information about TASQ 2.2 and its installation. The setup can be used
for a complete installation.
TASQ 2.2 is a modern multitier Client/Server application. The server side consists of the
following core components:
• The Compass 4.0 modular application server based on Karaf
• Hibernate ORM
• PostgreSQL 10.x
The TASQ 2.2 client is a dedicated client application that is based on the Eclipse RCP platform.
The client can be installed from the USB included in the product.

2 TASQ 2.2 features

TASQ 2.2 is a Client/Server solution aimed at customers performing targeted screening and
quantification of small molecules. The package contains installations for both client and server
and includes three client software licenses.
Target compounds can be screened and quantified in batches of LC-MS runs through high-
resolution Extracted Ion Chromatograms (EIC). Visualization of deviation in mass accuracy,
isotopic pattern — and where required, retention time — enables rapid verification of the results
by the user. In addition, the display of chromatograms, mass spectra and statistical plots
simplifies data interpretation from complete batches. Chromatographic peaks can be manually
integrated by the user and the generated data can be exported as reports and spreadsheet
documents.

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3 Installation procedure
3.1 Initial installation of TASQ
The TASQ Server uses PostgreSQL software. PostgreSQL will be installed automatically during
the TASQ setup:
• Install TASQ Server Modules (including PostgreSQL) from the product DVD
• Install TASQ Client application on target computer from the product DVD
• Log in as administrator and install the license key (Admin Preferences > System
Information > Licenses)

3.2 TASQ server / workstation requirements

• A high-performance computer (at least 8 GB RAM) is recommended.
• The software must be installed on a Windows 10 64-bit PC.
• Database system (RDBMS): PostgreSQL [Link] (included in the setup) x64.
• If you intend to process the data on the TASQ server computer at least two 1TB better 2TB
hard disc drives are recommended. Raw data and TASQ DB shall be located on two
different physical hard drives.
• For a computer with two separate hard drive partitions shall be configured as follows:
o Partition C and E on first hard drive, Partition D the entire second hard drive
o C:\ with 100 GB for the OS and the TASQ server and client SW installation
o E:\ with the remaining space ~900 GB for the TASQ database storage
o D:\ for the database backup and raw data storage
• It is recommended to use one SSD drive with at least 1 TB. The SSD shall be configured
to have the partition with the OS typically drive C:\ with 100 GB and the remaining 900 GB
for the TASQ database storage typically drive E:\.
Storing the TASQ result database on an SSD will improve the performance of adding and
reading processing results.
The TASQ installation DVD contains the server setup, which will install the application server
components and the database components.

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3.3 TASQ server / workstation installation

• Choose Server Full Installation on a fresh TASQ server. Click Next to continue the
installation.
• In the following dialog, choose the location for the database content. This directory should
be located on a local hard disk with at least 1 TB free space.
• Port settings for http and CORBA access to the server are preconfigured and should only
be changed if necessary.
• The storage location of the backup files should be chosen carefully. With increasing usage
of TASQ, larger quantities of storage space will be required for backup files. Backup files
can be stored on a remote file server. The backup tool will back up files on a regular basis
(daily, weekly, monthly, and yearly). Consider moving backup files automatically to a
remote location to reduce the space on TASQ server computer. This option is part of
software installation.
• For more details refer to the TASQ 2.2 Installation Guide available on the installation
media.

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TASQ 2.2

After the installation has finished, the following directory is available:

C:\Program Files\Bruker\Bruker Compass Server.

3.4 TASQ client installation

The TASQ installation DVD contains the client installation in the TASQ folder. The following
screenshots illustrate the client installation using the installation wizard:

The following windows are displayed and the user is required to accept the Bruker End User
License Agreement (EULA).

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Note For data processing Bruker MS Data Processing software is installed automatically. In
addition, a matching Java Runtime Environment (JRE) is provided.
Note tsqCommandsServer is not installed automatically. In order to process ion trap data or
to use the old processing for TOF data, choose the installation option for
tsqCommandsServer from the CD Browser.
After installation is complete, start the TASQ client using the icon on the desktop or by selecting
Start > Programs > Bruker > TASQ.

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3.5 Licensing TASQ

In order to use TASQ product you have to register a TASQ SW license. Otherwise, you will get
the following error message indicating that no valid license was found for TASQ.

For instructions on how to license Bruker Daltonics software please refer to the Bruker Software
Licensing User Manual provided on your TASQ 2.2 installation media.
If you have not received a license ticket yet, please send an email to [Link]@[Link],
and include the following information:
• Your name, institution and postal address;
• The name(s) and version(s) of the software product(s) you have purchased;
• Your order number.

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4 Site specifications and data security

4.1 Compatibility issues
• Do not install the server parts of TASQ, ProteinScape, BioPharma Compass, MALDI
Biotyper and/or Compass OpenAccess on the same computer!
• If DataAnalysis is used to review results, version 5.2 is mandatory.
4.2 Data format issues
TASQ supports:
• ESI-TOF data from LC-MS/LC-MS/MS or other separation techniques (for example, GC)
that has been acquired with a HyStar Compass 1.x system or newer
• Data acquired with MS Workstation or tqControl on Bruker TQ instruments ̶ This means
that a valid [Link] file must exist for each imported analysis or from TQ
systems that has been acquired with MS Workstation or tqControl.
4.3 Security issues
Bruker is not responsible for protection of the computer against viruses, Trojan horses, and
other malware. We strongly recommend installing supported antivirus software (see section
4.3.2) and using a firewall.
The following environment is required for the TASQ server to function properly.
4.3.1 Network connection
A TCP/IP network connection between the clients and the server is required. Minimum Network
Speed should be 10 Mbps with latency of <100 ms.

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TASQ 2.2

4.3.2 Antivirus software

Symantec TM Endpoint Protection 14 (not part of the product) is supported.
TASQ does not usually have an issue with antivirus software, but there may be an issue with
integrated solutions containing features such as antivirus software, antispyware, firewall,
intrusion prevention, device and application control, and so on.
Before you install any non-Bruker program, we recommend creating an image of the running
system. Afterward, install the new software, perform changes, then reboot the system, and test
the Bruker programs, especially the network connections.
4.3.3 Firewall issues
The TASQ Server should be protected against unauthorized access from the Internet by a
dedicated firewall system. Installation of firewall software on the TASQ server is not
recommended.
Note Please make sure that the firewall software is deactivated during the installation of
TASQ.
Bruker is not responsible for the protection of the computer systems in the customer’s
environment.

5 Manuals
The TASQ User Manual is provided as a PDF on the installation USB. The information in the
document is available as searchable context-sensitive help in the TASQ client using the F1 Key
on any selected view.

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6 Known problems / bugs

6.1 Database systems have been updated — incompatibilities
The installation of the TASQ Server overwrites existing database systems from previous
installations of MALDI Biotyper, Compass OpenAccess 1.x, or ProteinScape 4.x and earlier.
Therefore, do not install TASQ on the same machine as Compass OpenAccess 1.x,
ProteinScape 4.x or MALDI Biotyper.

6.2 Batch processing fails

Normally this is caused by a loss of communication of [Link] or in case

[Link] stops unexpectedly. Open the Windows Task Manager and check
whether there are three instances of [Link] running.

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If batch processing fails, one of the instances shows a high CPU usage or only one
[Link] process is running.
In the former case, right-click each [Link] process and select End
Process from the shortcut menu.
Stop and restart the TASQ Client and make sure that three instances of
[Link] appear.

Expert workaround: Open the command shell and type: "C:\Program files\Bruker
Daltonik\TSQCommandsServer\[Link]" --reprocessing
Do not close the command shell as long as you are working with TASQ Client.

For manual integration a similar workaround exists:

Open the command shell and type: "C:\Program files\Bruker
Daltonik\TSQCommandsServer\[Link]" –manualIntegration
Do not close the command shell as long as you are working with TASQ Client.

Another cause may be that the environment variable TSQ_COMMANDS_HOME is not defined.
Open a command shell and type “set tsq”. If you receive the following response:
C:\Program Files\Bruker Daltonik\TSQCommandsServer>set tsq
Environment variable tsq not defined
go to Control Panel > All Control Panel Items > System and select Advanced system
settings > Environment Variables. In the lower pane for system variables select New. Enter
“TSQ_COMMANDS_HOME” as variable name. For the variable value enter the path where
[Link] is installed. This is typically: “C:\Program Files\Bruker
Daltonik\TSQCommandsServer”.

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If you are using workflows based on Bruker MS Data Processing service, restart that service
from Services.

6.3 No more licenses left

If the number of running clients connected to the server exceeds the number of available
licenses an error message is generated:

This may also be the case when the TASQ client stops in an error situation. Log on as
administrator and close an open connection of a user by right-clicking a line in the table of
logged in users and selecting Remove session from the shortcut menu. After removal of the
session you will be able to log in as user once again.

6.4 Update problems in Chromatograms view

From time to time the Chromatograms view does not reflect the actual state of the respective
results table. Change the selection in the table to change the content of the Chromatograms
view.

6.5 Working with different methods

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TASQ 2.2

Working with different methods within the same batch is not supported. If you need to test the
influence of different method settings, the recommended procedure is to import the batch
multiple times and test the various method settings in the different imported batches. When
importing the batch multiple times, you can choose a subset of the sample data.

6.6 No results although processing was successful

From time to time processing results may not be visible immediately after processing, even
though the processing was successful. In such cases, the following message is sent to the
server log file:

e46d-41ee-bd21-c5b0a26aafc3]: …

[2016-04-19 [Link].134] WARN Atomikos:2

[Link] Timeout/setRollbackOnly of
ACTIVE coordinator !

Or

[2016-04-20 [Link].581] DEBUG RequestProcessor-40

[Link]
Creating chromatogram peak with id [2254b970-ac3e-4370-bfc0-
e3a6721368a7]
[2016-04-20 [Link].617] ERROR taskExecutor-4
[Link]
[Link]: Error performing
'[Link]
eResultsOfAnalysis([Link] analysisId)' -->
[Link]: JTA
transaction unexpectedly rolled back (maybe due to a timeout); nested
exception is [Link]: Prepare: NO vote
[2016-04-20 [Link].649] ERROR taskExecutor-4
[Link]
at
[Link]
tiveResultsOfAnalysis([Link])
…
In client log file a similar observation can be found:!ENTRY
[Link] 4 2 2016-04-20 [Link].677
!MESSAGE Problems occurred when invoking code from plug-in:
"[Link]".

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!STACK 0
[Link]: Prepare: NO vote
at
[Link]
hodInfo([Link])
at
[Link]
odInfo([Link])
at
[Link]
oAndMethod([Link])
at
[Link]
([Link])

You can increase the time out to 180 s – 300 s by adding the following lines:
# the *default* timeout for transactions (in seconds)
[Link]=600

# the *maximum* timeout value for (user) transactions (in seconds)

[Link]=600

to the file:
C:\Program Files\Bruker\Bruker Compass Server\etc\[Link]

To activate this setting, you must restart the server. Either restart the computer or go to
Services, select Bruker Compass Server and select Restart.
If raw data has been moved or deleted, no results will be obtained.

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6.7 Import of tasqMethod fails

Occasionally the import of a tasqMethod fails due to a large number of analytes. The import
ends and reports “TASQ method import error”.

In the server log file you can find following entries indicating that a timeout was reached.

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TASQ 2.2

[2016-07-11 [Link].311] DEBUG RequestProcessor-

45 [Link]
Updating compounds [1238]
[2016-07-11 [Link].010] DEBUG ggingNotificationScheduler-1
[Link] Foun
d 0 event logs to be notified.
[2016-07-11 [Link].123]
WARN Atomikos:1 [Link]
Handler Timeout/setRollbackOnly of ACTIVE
coordinator !
You can either increase the timeout thresholds as described in section 6.6 or change the import
options to “No merging”.

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6.8 TASQ client crashes when a report is generated

This is typically caused by a missing PDF viewer. To resolve the problem, install a PDF viewer.

6.9 Quantitation view does not show a calibration function and

calibration table is empty
If you have selected a batch and an analyte, the quantitation view shows a calibration function
and the table is filled with the respective information. If this view is empty, most probably you
have not assigned the sample type calibrant to the measured calibrator standards. You can
assign the sample type in the batch navigator tree by right-clicking the appropriate analysis
node and selecting Update Sample Type from the shortcut menu.

6.10 If no concentration for an internal standard is specified, the data

point will not be taken into account for regression calculation or no
quantities can be calculated for this determination
If you are calculating concentrations based on a calibration function relative to an internal
standard, the software tries to retrieve the specified concentration of an internal standard in the
respective sample for which the concentration is to be calculated. If you have not specified the
concentration for the internal standard for the respective sample, the data point will be ignored
for the calculation of regression function or for quantitation calculation. In Batch Concentrations
view the cell for this analyte and data set will be highlighted. In server log a log entry will give
you details for which analyte and data set the concentration value is not defined.

6.11 HyStar cannot start sequence of TASQ batch if tasq processing

service is not started
HyStar reports that required task executor is not available. In such a case restart Bruker MS
Data Processing service in [Link].

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6.12 Chromatographic peaks are not centered in reports

If your computer is not configured to us-en local settings of decimal separators you may get
chromatographic peaks reported which are not centered properly as shown below.
To fix this problem you can make following change in C:\Program Files\Bruker\Bruker
Compass Server\bin\[Link]
Exchange line:
set JMX_OPTS=-Xmx1024m -XX:MaxPermSize=768m
by
set JMX_OPTS=-Xmx1024m -XX:MaxPermSize=768m -[Link]=en
-[Link]=US

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6.13 Exporting of large tables containing icons to Excel file format is

time consuming
Alternatively, export batch results using the Export batch to LIMS command available from
context menu of Batch Navigator or from toolbar of Batch Summary view.

6.14 Processing data on a network drive

When you want to process data with Bruker MS Data Processing service which is located on a
network drive you have to configure Bruker MS Data Processing service to logon with user
credentials which allows access to read and write data located on the network drive. By default
Bruker MS Data Processing runs with local system user credentials. To change the user for the
service open Services from Windows Start.

6.15 Running TASQ TQ-Batch Processor on a remote computer

If you want to run TASQ TQ-Batch Processor on a client computer connected remotely to
Compass Server, you have to specify corbaServerName=remote-compass-server-name and
stationId in [Link] file. This file is located in C:\BrukerWS.
If you try to run TASQ TQ-Batch Processor on a remote computer and you have not configured
the [Link], the processing tool will not start on double-click.

6.16 Running automatic reporting feature does not work for TOF
workflow
You can specify reports to be used in automation workflow for generating reports automatically
after the data have been acquired and processed. This feature is only available for TQ
workflows within tqControl.

6.17 Exporting result data to LIMS in automation

In order to export results to LIMS in automation you have to select the option Single file for
batch in the Workflow settings tab of Method Editor. Otherwise, no data will be exported.

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6.18 Analytes with expected retention time = 0 are scored with failed for
RT Score instead of RT Score not available (grey)

6.19 If Ion Ratio deviates too much from expected Ion Ratio the Ion
Score renders red also for TOF data sets

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6.20 Sometimes the GUI got scrambled

In some occasions the GUI got scrambled, views can not be opened anymore or shows an error
message or in result tables values are shown in wrong columns and toolbar icons are missing.
To resolve this situation you have to navigate with the file explorer to “%appdata%\Bruker
Daltonik\Server Access\tsq\workspaces” and delete the content for the TASQ user
which have observed the defect state of GUI, e.g., demo@localhost.

6.21 Installation of TASQ and/or MCube server setup seems to be frozen

In case that the server setup does not proceed for a long time, this may be caused by the
following typical situations:
a. Windows is updating the system. In that case wait until the Windows update is finished
and proceed with the installation.
b. An automatic backup of Bruker Compass database is conducted. In that case check
with Task Manager whether there is a process with name pg-dump being active. Either
wait until the backup is finished or end the pg-dump task in Task Manager.

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6.22 After upgrading TASQ server the Bruker Compass Server does not
start timely
If the Bruker Compass Server takes a lot time for starting up this may be caused by an
automatic update of TASQ methods from previous TASQ method versions to the most recent
TASQ method version 2.2. This process is lengthy and can take up to several hours. It may be
necessary to restart the Bruker Compass Server more one once.

6.23 Upgrade to TASQ method version 2.2 alters smoothing width

To make the smoothing comparable to DataAnalysis and interpret the smoothing width correctly
in seconds, the behaviour of the smoothing algorithm in TASQ was changed and the smoothing
width is multiplied internally by a factor of ~2.4. Old TASQ methods which use that smoothing
algorithm are changed in such way that the smoothing widths are divided by a factor of ~2.4.

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7 Reporting bugs to Bruker

If you discover a bug in the software, Bruker will normally request the log files. Log files are
generated at various locations. There are server log files, client log files, and log files generated
from [Link]. You find these files on the respective computer at the
following locations:
Server: Typically C:\Program Files\Bruker\Bruker Compass Server\data\log
Client: Typically C:\Users\<current Windows User>\AppData\Roaming\Bruker
Daltonik\Server Access\tsq\workspaces
TSQCommandsServer: Typically C:\Users\<current Windows User>\TASQ
NUPF: Typically C:\BDalSystemData\NupfTaskExecutor\logs

To collect the relevant log files use the command “Create Station Report” which is located in the
context menu of the Help menu in the right corner of the Bruker ribbon.

If you are connected to a remote server you have to collect the server log files seperately. In
case client and server are located on the same computer the station report will contain the
server log file.

Descriptions and specifications supersede all previous information and are subject to change
without notice.
Copyright © 2019, Bruker Daltonik GmbH, November 2019

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